Deep sequencing analysis of viral infection and evolution allows rapid and detailed characterization of viral mutant spectrum.

Abstract : The study of RNA virus populations is a challenging task. Each population of RNA virus is composed of a collection of different, yet related genomes often referred to as mutant spectra or quasispecies. Virologists using deep sequencing technologies face major obstacles when studying virus population dynamics, both experimentally and in natural settings due to the relatively high error rates of these technologies and the lack of high performance pipelines. In order to overcome these hurdles we developed a computational pipeline, termed ViVan (Viral Variance Analysis). ViVan is a complete pipeline facilitating the identification, characterization and comparison of sequence variance in deep sequenced virus populations. Applying ViVan on deep sequenced data obtained from samples that were previously characterized by more classical approaches, we uncovered novel and potentially crucial aspects of virus populations. With our experimental work, we illustrate how ViVan can be used for studies ranging from the more practical, detection of resistant mutations and effects of antiviral treatments, to the more theoretical temporal characterization of the population in evolutionary studies. Freely available on the web at http://www.vivanbioinfo.org : nshomron@post.tau.ac.il Supplementary data are available at Bioinformatics online.
Document type :
Journal articles
Complete list of metadatas

Cited literature [68 references]  Display  Hide  Download

https://hal-pasteur.archives-ouvertes.fr/pasteur-01182469
Contributor : Antonio V. Borderia <>
Submitted on : Friday, July 31, 2015 - 3:22:35 PM
Last modification on : Wednesday, June 26, 2019 - 7:24:02 PM
Long-term archiving on: Sunday, November 1, 2015 - 10:42:51 AM

File

Bioinformatics-2015-Isakov-214...
Publication funded by an institution

Identifiers

Collections

Citation

Ofer Isakov, Antonio V Bordería, David Golan, Amir Hamenahem, Gershon Celniker, et al.. Deep sequencing analysis of viral infection and evolution allows rapid and detailed characterization of viral mutant spectrum.. Bioinformatics (Oxford, England), 2015, 31 (13), pp.2141-50. ⟨10.1093/bioinformatics/btv101⟩. ⟨pasteur-01182469⟩

Share

Metrics

Record views

359

Files downloads

624